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  <h1>Source code for data.graph_data_layer</h1><div class="highlight"><pre>
<span></span><span class="c1"># TODO: variable length batching</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>


<span class="kn">from</span> <span class="nn">openchem.utils.graph</span> <span class="k">import</span> <span class="n">Graph</span>

<span class="kn">from</span> <span class="nn">rdkit</span> <span class="k">import</span> <span class="n">Chem</span>

<span class="kn">from</span> <span class="nn">torch.utils.data</span> <span class="k">import</span> <span class="n">Dataset</span>
<span class="kn">from</span> <span class="nn">openchem.data.utils</span> <span class="k">import</span> <span class="n">read_smiles_property_file</span><span class="p">,</span> <span class="n">sanitize_smiles</span>


<div class="viewcode-block" id="GraphDataset"><a class="viewcode-back" href="../../api-docs/data.html#data.graph_data_layer.GraphDataset">[docs]</a><span class="k">class</span> <span class="nc">GraphDataset</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">get_atomic_attributes</span><span class="p">,</span> <span class="n">node_attributes</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span>
                 <span class="n">cols_to_read</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
        <span class="nb">super</span><span class="p">(</span><span class="n">GraphDataset</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
        <span class="n">data_set</span> <span class="o">=</span> <span class="n">read_smiles_property_file</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">cols_to_read</span><span class="p">,</span>
                                                 <span class="n">delimiter</span><span class="p">)</span>
        <span class="n">data</span> <span class="o">=</span> <span class="n">data_set</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
        <span class="n">target</span> <span class="o">=</span> <span class="n">data_set</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
        <span class="n">clean_smiles</span><span class="p">,</span> <span class="n">clean_idx</span> <span class="o">=</span> <span class="n">sanitize_smiles</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
        <span class="n">target</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">target</span><span class="p">)</span><span class="o">.</span><span class="n">T</span>
        <span class="n">max_size</span> <span class="o">=</span> <span class="mi">0</span>
        <span class="k">for</span> <span class="n">sm</span> <span class="ow">in</span> <span class="n">clean_smiles</span><span class="p">:</span>
            <span class="n">mol</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromSmiles</span><span class="p">(</span><span class="n">sm</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetNumAtoms</span><span class="p">()</span> <span class="o">&gt;</span> <span class="n">max_size</span><span class="p">:</span>
                <span class="n">max_size</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetNumAtoms</span><span class="p">()</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">[</span><span class="n">clean_idx</span><span class="p">,</span> <span class="p">:]</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">graphs</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">node_feature_matrix</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">adj_matrix</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="k">for</span> <span class="n">sm</span> <span class="ow">in</span> <span class="n">clean_smiles</span><span class="p">:</span>
            <span class="n">graph</span> <span class="o">=</span> <span class="n">Graph</span><span class="p">(</span><span class="n">sm</span><span class="p">,</span> <span class="n">max_size</span><span class="p">,</span> <span class="n">get_atomic_attributes</span><span class="p">)</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">node_feature_matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
                <span class="n">graph</span><span class="o">.</span><span class="n">get_node_feature_matrix</span><span class="p">(</span><span class="n">node_attributes</span><span class="p">,</span> <span class="n">max_size</span><span class="p">))</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">adj_matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">graph</span><span class="o">.</span><span class="n">adj_matrix</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">num_features</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">node_feature_matrix</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>

    <span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">)</span>

    <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
        <span class="n">sample</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;adj_matrix&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">adj_matrix</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;float32&#39;</span><span class="p">),</span>
                  <span class="s1">&#39;node_feature_matrix&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">node_feature_matrix</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;float32&#39;</span><span class="p">),</span>
                  <span class="s1">&#39;labels&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;float32&#39;</span><span class="p">)}</span>
        <span class="k">return</span> <span class="n">sample</span></div>

</pre></div>

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